can someone help me understand what it is? I know it's used for DLP Link for the glasses to know how to sync for which eye but the way people word it you would think it's a visible flash on the screen.. from what I also seem to understand in DLP link the clear section of the color wheel is used for DLP Link? If that's the case why is the screen always dimmer in 3D content?

The DLP link flash is visable without the glasses on. Not all DLP link flash is white the HD33 is red. The shutter glasses have both lenses blacked out during the flash and alternate for your 3D image causing the picture to be to be darker and are tinted darker when open dimming the picture more.